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Abera TA, Heiskanen J, Maeda EE, Muhammed MA, Bhandari N, Vakkari V, Hailu BT, Pellikka PKE, Hemp A, van Zyl PG, Zeuss D. Deforestation amplifies climate change effects on warming and cloud level rise in African montane forests. Nat Commun 2024; 15:6992. [PMID: 39143071 PMCID: PMC11324879 DOI: 10.1038/s41467-024-51324-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024] Open
Abstract
Tropical montane forest ecosystems are pivotal for sustaining biodiversity and essential terrestrial ecosystem services, including the provision of high-quality fresh water. Nonetheless, the impact of montane deforestation and climate change on the capacity of forests to deliver ecosystem services is yet to be fully understood. In this study, we offer observational evidence demonstrating the response of air temperature and cloud base height to deforestation in African montane forests over the last two decades. Our findings reveal that approximately 18% (7.4 ± 0.5 million hectares) of Africa's montane forests were lost between 2003 and 2022. This deforestation has led to a notable increase in maximum air temperature (1.37 ± 0.58 °C) and cloud base height (236 ± 87 metres), surpassing shifts attributed solely to climate change. Our results call for urgent attention to montane deforestation, as it poses serious threats to biodiversity, water supply, and ecosystem services in the tropics.
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Affiliation(s)
- Temesgen Alemayehu Abera
- Department of Environmental Informatics, Faculty of Geography, Philipps-Universität Marburg, Deutschhausstraße 12, 35037, Marburg, Germany.
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 68, FI-00014, Helsinki, Finland.
| | - Janne Heiskanen
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 68, FI-00014, Helsinki, Finland
- Finnish Meteorological Institute, P.O. Box 503, FI-00101, Helsinki, Finland
| | - Eduardo Eiji Maeda
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 68, FI-00014, Helsinki, Finland
- Finnish Meteorological Institute, P.O. Box 503, FI-00101, Helsinki, Finland
| | - Mohammed Ahmed Muhammed
- Department of Environmental Informatics, Faculty of Geography, Philipps-Universität Marburg, Deutschhausstraße 12, 35037, Marburg, Germany
- School of Earth Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Netra Bhandari
- Department of Environmental Informatics, Faculty of Geography, Philipps-Universität Marburg, Deutschhausstraße 12, 35037, Marburg, Germany
| | - Ville Vakkari
- Finnish Meteorological Institute, P.O. Box 503, FI-00101, Helsinki, Finland
- Atmospheric Chemistry Research Group, Chemical Resource Beneficiation, North-West University, Potchefstroom, South Africa
| | - Binyam Tesfaw Hailu
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 68, FI-00014, Helsinki, Finland
- School of Earth Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Petri K E Pellikka
- Department of Geosciences and Geography, University of Helsinki, P.O. Box 68, FI-00014, Helsinki, Finland
- State Key Laboratory for Information Engineering in Surveying, Mapping and Remote Sensing, Wuhan University, Wuhan, 430079, China
| | - Andreas Hemp
- Department of Plant Systematics, University of Bayreuth, 95440, Bayreuth, Germany
| | - Pieter G van Zyl
- Atmospheric Chemistry Research Group, Chemical Resource Beneficiation, North-West University, Potchefstroom, South Africa
| | - Dirk Zeuss
- Department of Environmental Informatics, Faculty of Geography, Philipps-Universität Marburg, Deutschhausstraße 12, 35037, Marburg, Germany
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2
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Ozu M, Galizia L, Alvear-Arias JJ, Fernández M, Caviglia A, Zimmermann R, Guastaferri F, Espinoza-Muñoz N, Sutka M, Sigaut L, Pietrasanta LI, González C, Amodeo G, Garate JA. Mechanosensitive aquaporins. Biophys Rev 2023; 15:497-513. [PMID: 37681084 PMCID: PMC10480384 DOI: 10.1007/s12551-023-01098-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/04/2023] [Indexed: 09/09/2023] Open
Abstract
Cellular systems must deal with mechanical forces to satisfy their physiological functions. In this context, proteins with mechanosensitive properties play a crucial role in sensing and responding to environmental changes. The discovery of aquaporins (AQPs) marked a significant breakthrough in the study of water transport. Their transport capacity and regulation features make them key players in cellular processes. To date, few AQPs have been reported to be mechanosensitive. Like mechanosensitive ion channels, AQPs respond to tension changes in the same range. However, unlike ion channels, the aquaporin's transport rate decreases as tension increases, and the molecular features of the mechanism are unknown. Nevertheless, some clues from mechanosensitive ion channels shed light on the AQP-membrane interaction. The GxxxG motif may play a critical role in the water permeation process associated with structural features in AQPs. Consequently, a possible gating mechanism triggered by membrane tension changes would involve a conformational change in the cytoplasmic extreme of the single file region of the water pathway, where glycine and histidine residues from loop B play a key role. In view of their transport capacity and their involvement in relevant processes related to mechanical forces, mechanosensitive AQPs are a fundamental piece of the puzzle for understanding cellular responses.
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Affiliation(s)
- Marcelo Ozu
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Luciano Galizia
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Juan José Alvear-Arias
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
| | - Miguel Fernández
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
| | - Agustín Caviglia
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Rosario Zimmermann
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Florencia Guastaferri
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
- Present Address: Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET-UNR), Rosario, Argentina
| | - Nicolás Espinoza-Muñoz
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
| | - Moira Sutka
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lorena Sigaut
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina
- Instituto de Física de Buenos Aires (IFIBA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Lía Isabel Pietrasanta
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Física, Buenos Aires, Argentina
- Instituto de Física de Buenos Aires (IFIBA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Carlos González
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
- Department of Physiology and Biophysics, Miller School of Medicine, University of Miami, Miami, FL 33136 USA
- Present Address: Molecular Bioscience Department, University of Texas, Austin, TX 78712 USA
| | - Gabriela Amodeo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Biodiversidad y Biología Experimental, Buenos Aires, Argentina
- Instituto de Biodiversidad y Biología Experimental y Aplicada (IBBEA), Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - José Antonio Garate
- Interdisciplinary Center of Neurosciences of Valparaiso, University of Valparaiso, CINV, 2360102 Valparaíso, Chile
- Millennium Nucleus in NanoBioPhysics, Santiago, Chile
- Facultad de Ingeniería, Arquitectura y Diseño, Universidad San Sebastián, Bellavista, Santiago, Chile
- Centro Científico y Tecnológico de Excelencia Ciencia y Vida, Universidad San Sebastián, 7750000 Santiago, Chile
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3
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Mata-Guel EO, Soh MCK, Butler CW, Morris RJ, Razgour O, Peh KSH. Impacts of anthropogenic climate change on tropical montane forests: an appraisal of the evidence. Biol Rev Camb Philos Soc 2023; 98:1200-1224. [PMID: 36990691 DOI: 10.1111/brv.12950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/31/2023]
Abstract
In spite of their small global area and restricted distributions, tropical montane forests (TMFs) are biodiversity hotspots and important ecosystem services providers, but are also highly vulnerable to climate change. To protect and preserve these ecosystems better, it is crucial to inform the design and implementation of conservation policies with the best available scientific evidence, and to identify knowledge gaps and future research needs. We conducted a systematic review and an appraisal of evidence quality to assess the impacts of climate change on TMFs. We identified several skews and shortcomings. Experimental study designs with controls and long-term (≥10 years) data sets provide the most reliable evidence, but were rare and gave an incomplete understanding of climate change impacts on TMFs. Most studies were based on predictive modelling approaches, short-term (<10 years) and cross-sectional study designs. Although these methods provide moderate to circumstantial evidence, they can advance our understanding on climate change effects. Current evidence suggests that increasing temperatures and rising cloud levels have caused distributional shifts (mainly upslope) of montane biota, leading to alterations in biodiversity and ecological functions. Neotropical TMFs were the best studied, thus the knowledge derived there can serve as a proxy for climate change responses in under-studied regions elsewhere. Most studies focused on vascular plants, birds, amphibians and insects, with other taxonomic groups poorly represented. Most ecological studies were conducted at species or community levels, with a marked paucity of genetic studies, limiting understanding of the adaptive capacity of TMF biota. We thus highlight the long-term need to widen the methodological, thematic and geographical scope of studies on TMFs under climate change to address these uncertainties. In the short term, however, in-depth research in well-studied regions and advances in computer modelling approaches offer the most reliable sources of information for expeditious conservation action for these threatened forests.
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Affiliation(s)
- Erik O Mata-Guel
- School of Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Malcolm C K Soh
- National Park Boards, 1 Cluny Road, Singapore, 259569, Singapore
| | - Connor W Butler
- School of Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Rebecca J Morris
- School of Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
| | - Orly Razgour
- Biosciences, University of Exeter, Exeter, EX4 4PS, UK
| | - Kelvin S-H Peh
- School of Biological Sciences, University of Southampton, Highfield Campus, Southampton, SO17 1BJ, UK
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4
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Xing G, Zhang S, Zhu W, Ben T. Reply to the Correspondence on "Crystalline Porous Organic Salt for Ultrarapid Adsorption/Desorption-Based Atmospheric Water Harvesting by Dual Hydrogen Bond System". Angew Chem Int Ed Engl 2023; 62:e202215074. [PMID: 36658744 DOI: 10.1002/anie.202215074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Indexed: 01/21/2023]
Abstract
White et al., in a recent Correspondence, provided additional structural data to illustrate that CPOS-6 undergoes a single-crystal-to-single-crystal transformation during water adsorption/desorption. This finding gave a better understanding of the relevant experimental phenomena from the perspective of structural transformation and is a good complement to our previous results. However, we wish to emphasize that our research focuses on the kinetic behavior of water during ultrafast adsorption/desorption in nano-confined channels. Herein, we further interpret the rapid transport of water molecules in the nano-confined channels from the perspective of superfluidity.
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Affiliation(s)
- Guolong Xing
- Zhejiang Engineering Laboratory for Green Syntheses and Applications of Fluorine-Containing Specialty Chemicals, Institute of Advanced Fluorine-Containing Materials, Zhejiang Normal University, Jinhua, 321004, China.,Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, 321004, China
| | - Shuai Zhang
- Zhejiang Engineering Laboratory for Green Syntheses and Applications of Fluorine-Containing Specialty Chemicals, Institute of Advanced Fluorine-Containing Materials, Zhejiang Normal University, Jinhua, 321004, China.,Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, 321004, China
| | - Weidong Zhu
- Zhejiang Engineering Laboratory for Green Syntheses and Applications of Fluorine-Containing Specialty Chemicals, Institute of Advanced Fluorine-Containing Materials, Zhejiang Normal University, Jinhua, 321004, China.,Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, 321004, China
| | - Teng Ben
- Zhejiang Engineering Laboratory for Green Syntheses and Applications of Fluorine-Containing Specialty Chemicals, Institute of Advanced Fluorine-Containing Materials, Zhejiang Normal University, Jinhua, 321004, China.,Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, 321004, China
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5
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Ramírez BH, Cortés‐B R, Pinzón OP, Gómez L, Jacquin S, Hernández E, Quimbayo LA, Bogotá‐A RG. Cloud forests of the Orinoco River Basin (Colombia): Variation in vegetation and soil macrofauna composition along the hydrometeorological gradient. Biotropica 2023. [DOI: 10.1111/btp.13203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
Affiliation(s)
- Beatriz H. Ramírez
- Maestría en Manejo, Uso y Conservación del Bosque Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
- Centro de Estudios Ambientales de la Orinoquia ‐CEAO ABC Colombia Yopal Colombia
| | - Rocío Cortés‐B
- Maestría en Manejo, Uso y Conservación del Bosque Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
- Ingeniería Forestal Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
| | - Olga Patricia Pinzón
- Maestría en Manejo, Uso y Conservación del Bosque Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
- Ingeniería Forestal Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
| | - Laura Gómez
- Ingeniería Forestal Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
| | - Santiago Jacquin
- Ingeniería Forestal Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
| | - Eduardo Hernández
- Ingeniería Forestal Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
| | - Luz Angélica Quimbayo
- Ingeniería Forestal Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
| | - Raúl Giovanni Bogotá‐A
- Maestría en Manejo, Uso y Conservación del Bosque Universidad Distrital Francisco José de Caldas ‐UDFJC Bogotá Colombia
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6
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Mills SC, Socolar JB, Edwards FA, Parra E, Martínez-Revelo DE, Ochoa Quintero JM, Haugaasen T, Freckleton RP, Barlow J, Edwards DP. High sensitivity of tropical forest birds to deforestation at lower altitudes. Ecology 2023; 104:e3867. [PMID: 36082832 PMCID: PMC10078351 DOI: 10.1002/ecy.3867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/13/2022] [Accepted: 07/07/2022] [Indexed: 02/01/2023]
Abstract
Habitat conversion is a major driver of tropical biodiversity loss, but its effects are poorly understood in montane environments. While community-level responses to habitat loss display strong elevational dependencies, it is unclear whether these arise via elevational turnover in community composition and interspecific differences in sensitivity or elevational variation in environmental conditions and proximity to thermal thresholds. Here we assess the relative importance of inter- and intraspecific variation across the elevational gradient by quantifying how 243 forest-dependent bird species vary in sensitivity to landscape-scale forest loss across a 3000-m elevational gradient in the Colombian Andes. We find that species that live at lower elevations are strongly affected by loss of forest in the nearby landscape, while those at higher elevations appear relatively unperturbed, an effect that is independent of phylogeny. Conversely, we find limited evidence of intraspecific elevational gradients in sensitivity, with populations displaying similar sensitivities to forest loss, regardless of where they exist in a species' elevational range. Gradients in biodiversity response to habitat loss thus appear to arise via interspecific gradients in sensitivity rather than proximity to climatically limiting conditions.
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Affiliation(s)
- Simon C Mills
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Jacob B Socolar
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway.,Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
| | - Felicity A Edwards
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK.,RSPB Centre for Conservation Science, RSPB, Cambridge, UK
| | - Edicson Parra
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | | | | | - Torbjørn Haugaasen
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Robert P Freckleton
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Jos Barlow
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - David P Edwards
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
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7
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Hadidi H, Kamali R. Non-equilibrium molecular dynamics study of human aquaporin-2 in the static external electric fields. J Biomol Struct Dyn 2022; 40:10793-10801. [PMID: 34243696 DOI: 10.1080/07391102.2021.1950570] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
In this paper, non-equilibrium MD simulations (NEMD) of human aquaporin-2 (AQP2) in the presence of an external static electric field have been performed along + z and - z directions of the pore axis. The impacts of the electric field direction on the gating mechanism corresponding to the selectivity filter (SF) region of AQP2 have been studied. Besides, the effects of applied external electric field on the PMF profile of water molecules translocation, water permeability, and molecules dipole orientation are investigated. Our results showed that when the external electric field is implemented along the + z direction of the channels, the selectivity filter region is kept in the wide conformation for the majority of the time. Therefore, a remarkable increase in the overall water permeability can be seen compared to the case without any external electric field. This is in contrast to the effects of - z-directed electric field on the conformations of the selectivity filter, which induces mostly narrow conformations in this constriction region. A substantial higher energy barrier emerged in the middle of the AQP2's pores under the effect of -z-directed electric field in comparison with the zero and + z-directed electric field strengths, which is mainly ascribed to the deviation from bipolar dipole orientation within the AQP2's pores.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hooman Hadidi
- School of Mechanical Engineering, Shiraz University, Shiraz, Iran
| | - Reza Kamali
- School of Mechanical Engineering, Shiraz University, Shiraz, Iran
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8
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Zhao B, Yin Q, Fei Y, Zhu J, Qiu Y, Fang W, Li Y. Research progress of mechanisms for tight junction damage on blood-brain barrier inflammation. Arch Physiol Biochem 2022; 128:1579-1590. [PMID: 32608276 DOI: 10.1080/13813455.2020.1784952] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Inflammation in the central nervous system (CNS) contributes to disease pathologies by disrupting the integrity of the blood-brain barrier (BBB). Tight junctions (TJ) are a key component of the BBB. Following hypoxic-ischaemic or mechanical injury to the brain, inflammatory mediators are released such as cytokines, chemokines, and growth factors. Simultaneously, matrix metalloproteinases (MMPs) are released which can degrade TJ proteins. Subsequently, the function and morphology of the BBB are disrupted, which allows immune cells an opportunity to enter into the brain parenchyma. This review summarises the information on the role of TJ protein families in the BBB and provides a comprehensive summary of the mechanisms whereby inflammation breaks down the BBB by increasing degradation of TJ proteins.
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Affiliation(s)
- Bo Zhao
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Qiyang Yin
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yuxiang Fei
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Jianping Zhu
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yanying Qiu
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Weirong Fang
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
| | - Yunman Li
- State Key Laboratory of Natural Medicines, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, People's Republic of China
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9
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Berrios HK, Coronado I, Marsico TD. High species richness and turnover of vascular epiphytes is associated with water availability along the elevation gradient of Volcán Maderas, Nicaragua. Ecol Evol 2022; 12:e9501. [PMID: 36440308 PMCID: PMC9682193 DOI: 10.1002/ece3.9501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 09/08/2022] [Accepted: 10/24/2022] [Indexed: 11/24/2022] Open
Abstract
Research that has been conducted documenting species richness patterns on tropical mountains has resulted in conflicting observations: monotonic declines with increasing elevation, monotonic increases with increasing elevation, and a mid-elevation "bulge." Currently, it is unclear if these differences are due to environmental differences among study areas, the taxonomic groups or ecological groups (e.g., growth form) sampled, or the scale of study along elevation gradients. Because of the difficulty in sampling and identifying canopy-dwelling plants, the number of inventories quantifying tropical epiphytes is relatively limited and recent. In this study, we provide a detailed qualitative and quantitative assessment of the vascular epiphyte flora and its spatial distribution on Volcán Maderas, Isla de Ometepe, Nicaragua, including weather and environmental measurements along the entire elevation gradient of the volcano. We sampled epiphytes in five distinct forest types associated with increasing elevation as follows: dry forest, humid forest, wet forest, cloud forest, and elfin forest. Five weather stations were placed along the elevation gradient for us to relate observed patterns to environmental conditions. A mid-elevation peak in species richness was detected for all vascular epiphytes at approximately 1000 m in elevation (cloud forest), yet epiphyte abundance increased with increasing elevation. In total we identified 206 taxa of vascular epiphytes belonging to 26 families and 73 genera. The most species-rich family was the Orchidaceae with 55 species for the entire elevation gradient, followed by Bromeliaceae (29 species), Araceae (23), Polypodiaceae (25), Dryopteridaceae (16), and Piperaceae (11), with all other families represented by fewer than 10 species each. We found that richness patterns differ phylogenetically across epiphyte groups, possibly due to different adaptive strategies, and species for the most part appear to be narrowly distributed within specific habitat zones along the elevation gradient. Variables associated with moisture, precipitation, humidity, mist, or cloud cover are key to understanding the observed patterns.
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Affiliation(s)
- Hazel K. Berrios
- Department of Biological SciencesArkansas State University, State UniversityJonesboroArkansasUSA
| | - Indiana Coronado
- Universidad Nacional Autónoma de Nicaragua (UNAN‐León)LeónNicaragua
| | - Travis D. Marsico
- Department of Biological SciencesArkansas State University, State UniversityJonesboroArkansasUSA
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10
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Pluhackova K, Schittny V, Bürkner P, Siligan C, Horner A. Multiple pore lining residues modulate water permeability of GlpF. Protein Sci 2022; 31:e4431. [PMID: 36173178 PMCID: PMC9490802 DOI: 10.1002/pro.4431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/23/2022] [Accepted: 08/25/2022] [Indexed: 11/11/2022]
Abstract
The water permeability of aquaporins (AQPs) varies by more than an order of magnitude even though the pore structure, geometry, as well as the channel lining residues are highly conserved. However, channel gating by pH, divalent ions or phosphorylation was only shown for a minority of AQPs. Structural and in silico indications of water flux modulation by flexible side chains of channel lining residues have not been experimentally confirmed yet. Hence, the aquaporin "open state" is still considered to be a continuously open pore with water molecules permeating in a single-file fashion. Using protein mutations outside the selectivity filter in the aqua(glycerol)facilitator GlpF of Escherichia coli we, to the best of our knowledge, for the first time, modulate the position of the highly conserved Arg in the selectivity filter. This in turn enhances or reduces the unitary water permeability of GlpF as shown in silico by molecular dynamics (MD) simulations and in vitro with purified and reconstituted GlpF. This finding suggests that AQP water permeability can indeed be regulated by lipid bilayer asymmetry and the transmembrane potential. Strikingly, our long-term MD simulations reveal that not only the conserved Arg in the selectivity filter, but the position and dynamics of multiple other pore lining residues modulate water passage through GlpF. This finding is expected to trigger a wealth of future investigations on permeability and regulation of AQPs among others with the aim to tune water permeability for biotechnological applications.
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Affiliation(s)
- Kristyna Pluhackova
- Stuttgart Center for Simulation Science, Cluster of Excellence EXC 2075University of StuttgartStuttgartGermany
| | - Valentin Schittny
- Department of Biosystems Science and EngineeringEidgenössische Technische Hochschule (ETH) ZurichBaselSwitzerland
| | - Paul‐Christian Bürkner
- Stuttgart Center for Simulation Science, Cluster of Excellence EXC 2075University of StuttgartStuttgartGermany
| | | | - Andreas Horner
- Institute of BiophysicsJohannes Kepler UniversityLinzAustria
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11
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Saitoh Y, Suga M. Structure and function of a silicic acid channel Lsi1. FRONTIERS IN PLANT SCIENCE 2022; 13:982068. [PMID: 36172553 PMCID: PMC9510833 DOI: 10.3389/fpls.2022.982068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/24/2022] [Indexed: 05/26/2023]
Abstract
Silicon is a beneficial element for plant growth and production, especially in rice. Plant roots take up silicon in the form of silicic acid. Silicic acid channels, which belong to the NIP subfamily of aquaporins, are responsible for silicic acid uptake. Accumulated experimental results have deepened our understanding of the silicic acid channel for its uptake mechanism, physiological function, localization, and other aspects. However, how the silicic acid channel efficiently and selectively permeates silicic acid remains to be elucidated. Recently reported crystal structures of the silicic acid channel enabled us to discuss the mechanism of silicic acid uptake by plant roots at an atomic level. In this mini-review, we focus on the crystal structures of the silicic acid channel and provide a detailed description of the structural determinants of silicic acid permeation and its transport mechanism, which are crucial for the rational creation of secure and sustainable crops.
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Affiliation(s)
- Yasunori Saitoh
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan
| | - Michihiro Suga
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, Japan
- Graduate School of Natural Science and Technology, Okayama University, Okayama, Japan
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12
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Kefalew A, Soromessa T, Demissew S. Plant diversity and community analysis of Sele-Nono forest, Southwest Ethiopia: implication for conservation planning. BOTANICAL STUDIES 2022; 63:23. [PMID: 35851664 PMCID: PMC9294133 DOI: 10.1186/s40529-022-00353-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/02/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Studying the floristic diversity of a certain forest is a basic aspect of the design and management of forest vegetation; and consequently this study focused on the plant diversity and community analysis of the Sele-Nono forest. For the current study, plants were sampled from 90 plots using a stratified random sampling technique along the established strata of the study forest. In all the plots, both floristic and environmental data that were relevant to the study were collected following the state of the art. Based on the collected data, the community types, ordination, floristic diversity, and threats to the forest were analyzed using R-package and SPSS software. RESULTS Cluster analysis produced seven distinct community types which significantly differed among themselves (Cophentic correlation coefficient = 0.785, P < 0.001) of which community types 2 and 6 were relatively poor; whereas communities 1 and 4 were rich in terms of their species richness and diversity. In addition, Canonical Correspondence Analysis (CCA) suggests that a number of environmental factors such as altitude and slope (topographic factor), OM and N (edaphic factors) and disturbance were the main drivers for the current distribution of plant species and disparity in plant community composition in Sele-Nono forest. Moreover, the study revealed high beta diversity ([Formula: see text] >12) of plant species at the landscape level (i.e., throughout the study forest). Deforestation for agricultural land expansion and degradation through selective logging are the main threats to the Sele-Nono forest. CONCLUSIONS The present study revealed that the Sele-Nono forest is a large and heterogenous forest at the landscape level (150, 325.27 ha; [Formula: see text] >12). Moreover, it is one of the richest and diverse forest ecosystems in terms of plant biodiversity, and it could qualify to be labeled as a keystone ecosystem. However, currently it is exposed to a variety of threats. We recommend the forest to be developed into a biosphere reserve. We also recommend the prioritization of areas belonging to community types 2 and 6 of the forest for any possible conservation actions so as to maximize species richness and diversity of the native plants of the area.
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Affiliation(s)
- Alemayehu Kefalew
- Department of Plant Biology and Biodiversity Management, the National Herbarium, Addis Ababa University, P. O. Box 3434, Addis Ababa, Ethiopia.
- Department of Biology, Debre Markos University (DMU), P. O. Box 269, Debre Markos, Ethiopia.
| | - Teshome Soromessa
- Center for Environmental Science, Addis Ababa University, P. O. Box 1176, Addis Ababa, Ethiopia
| | - Sebsebe Demissew
- Department of Plant Biology and Biodiversity Management, the National Herbarium, Addis Ababa University, P. O. Box 3434, Addis Ababa, Ethiopia
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13
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Zimmermann MT. Molecular Modeling is an Enabling Approach to Complement and Enhance Channelopathy Research. Compr Physiol 2022; 12:3141-3166. [PMID: 35578963 DOI: 10.1002/cphy.c190047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Hundreds of human membrane proteins form channels that transport necessary ions and compounds, including drugs and metabolites, yet details of their normal function or how function is altered by genetic variants to cause diseases are often unknown. Without this knowledge, researchers are less equipped to develop approaches to diagnose and treat channelopathies. High-resolution computational approaches such as molecular modeling enable researchers to investigate channelopathy protein function, facilitate detailed hypothesis generation, and produce data that is difficult to gather experimentally. Molecular modeling can be tailored to each physiologic context that a protein may act within, some of which may currently be difficult or impossible to assay experimentally. Because many genomic variants are observed in channelopathy proteins from high-throughput sequencing studies, methods with mechanistic value are needed to interpret their effects. The eminent field of structural bioinformatics integrates techniques from multiple disciplines including molecular modeling, computational chemistry, biophysics, and biochemistry, to develop mechanistic hypotheses and enhance the information available for understanding function. Molecular modeling and simulation access 3D and time-dependent information, not currently predictable from sequence. Thus, molecular modeling is valuable for increasing the resolution with which the natural function of protein channels can be investigated, and for interpreting how genomic variants alter them to produce physiologic changes that manifest as channelopathies. © 2022 American Physiological Society. Compr Physiol 12:3141-3166, 2022.
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Affiliation(s)
- Michael T Zimmermann
- Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.,Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
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14
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Gotsch SG, Williams CB, Bicaba R, Cruz-de Hoyos R, Darby A, Davidson K, Dix M, Duarte V, Glunk A, Green L, Ferguson B, Muñoz-Elizondo K, Murray JG, Picado-Fallas I, Nӕsborg R, Dawson TE, Nadkarni N. Trade-offs between succulent and non-succulent epiphytes underlie variation in drought tolerance and avoidance. Oecologia 2022; 198:645-661. [DOI: 10.1007/s00442-022-05140-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 02/19/2022] [Indexed: 11/28/2022]
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15
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Chutia P, Das M, Goswami N, Choudhury M, Saha N, Sarma K. Deciphering the role of aquaporin 1 in the adaptation of the stinging catfish Heteropneustes fossilis to environmental hypertonicity by molecular dynamics simulation studies. J Biomol Struct Dyn 2022; 41:2075-2089. [PMID: 35040369 DOI: 10.1080/07391102.2022.2027272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
A thorough investigation of the water permeability of H. fossilis aquaporin 1 (hfAQP1) in a hypertonic environment can provide a useful insight into the understanding of the underlying molecular mechanism of its high tolerance to salinity. Here, we constructed a 3 D homology model of hfAQP1 by taking Bos taurus AQP1, AQP0, and human AQP2 as templates using I-TASSER. The model obtained has similar structural organizations with mammalian AQP1s in all aspects. We investigated the water permeability of the modeled hfAQP1 in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) membrane under neutral and 100 mM hypersalinity by subjecting each system to a 100 ns molecular dynamics simulation. Our results show that hypersalinity hinders water permeation across the membrane through the hfAQP1 channel. A change in the intermolecular distance between key residues of the ar/R selectivity filter along with charge redistribution resulted in the accommodation of only 2-6 water molecules inside the channel at once under hypersaline conditions. We investigated the mRNA expression pattern of hfaqp1 in osmoregulatory organs of H. fossilis in response to 100 mM hypertonicity by using qPCR analysis. The transcript was downregulated in kidney and GI tract, but upregulated in the Gills. Thus, the catfish survive in a hypertonic environment by reducing the transport of water in its cellular systems and downregulating the expression of the hfaqp1 gene. The results observed in our study can shed more light on the functionality of AQP1 in catfishes under salinity stress and aid in future researches on solving more gating mechanisms involved in its regulation.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyambada Chutia
- Animal Physiology and Biochemistry Laboratory, Department of Zoology, Gauhati University, Guwahati, Assam, India
| | - Manas Das
- Animal Physiology and Biochemistry Laboratory, Department of Zoology, Gauhati University, Guwahati, Assam, India.,Bioinformatics Infrastructure Facility, Gauhati University, Guwahati, Assam, India
| | - Nabajyoti Goswami
- Bioinformatics Infrastructure Facility, Assam Agriculture University, College of Veterinary Science, Khanapara, Guwahati, Assam, India
| | - Manisha Choudhury
- Bioinformatics Infrastructure Facility, Gauhati University, Guwahati, Assam, India.,Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Nirmalendu Saha
- Biochemical Adaptation Laboratory, Department of Zoology, North Eastern Hill University, Meghalaya, Shillong, India
| | - Kishore Sarma
- Bioinformatics Infrastructure Facility, Gauhati University, Guwahati, Assam, India
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16
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Ebrahimi M, Foroutan M. High-Performance Biomimetic Water Channel: The Constructive Interplay of Interaction Parameters and Hydrophilic Doping Levels. J Phys Chem B 2021; 125:11566-11581. [PMID: 34615355 DOI: 10.1021/acs.jpcb.1c04507] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In this study, we introduce a superfast biomimetic water channel mimicking the hydrophobicity scales of the Aquaporin (AQP) pore lining. Molecular dynamics simulation is used to scrutinize the impact of hydrophilic doping level in the nanotube and the water-wall interaction strength on water permeability. In the designed biomimetic channel, the constructive interplay of Lennard-Jones (LJ) ε parameters and hydrophilic doping levels increased the possibility of ultrafast water transport. Moreover, a unique set of LJ parameters is discovered for each biomimetic channel with different hydrophilic doping levels, enhancing water permeation. Inside high-performance biomimetic channels, water distribution surprisingly implies a varying pore geometry that narrows down in the middle, mimicking the pattern obtained from GplF pore analysis, evoking the narrow pore induced by the aromatic/arginine selectivity filter. This exciting accordance occurred as a result of tailoring specific hydrophilic arrays within the hydrophobic channel backbone by mimicking the AQP pore interior. The main takeaway of hydrophilic doping arrays implanted within the hydrophobic nanotube is to break the large barrier in the water-wall vdW energy profile into multiple reduced ones to increase water conduction. Consequently, the "water jumping" phenomenon in the middle of the biomimetic channel occurs under specific circumstances. The biomimetic channel with the highest value of water permeability of about 13.67 ± 0.66 × 10-13 cm3·s-1 exhibits the best mechanism for artificial water channels (AWCs), serving superfast water transport considering the low entrance barrier and weak water-wall interaction.
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Affiliation(s)
- Mina Ebrahimi
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran 1417935840, Iran
| | - Masumeh Foroutan
- Department of Physical Chemistry, School of Chemistry, College of Science, University of Tehran, Tehran 1417935840, Iran
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17
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Gonzalez MA, Zaragoza A, Lynch CI, Sansom MSP, Valeriani C. Influence of water models on water movement through AQP1. J Chem Phys 2021; 155:154502. [PMID: 34686053 DOI: 10.1063/5.0063986] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are responsible for enabling water permeation through the cell membrane. AQPs are highly selective, allowing only water and relatively small polar molecules to cross the membrane. Experimentally, estimation of water flux through membrane proteins is still a challenge, and hence, accurate simulations of water permeation are of particular importance. We present a numerical study of water diffusion through AQP1 comparing three water models: TIP3P, OPC, and TIP4P/2005. Bulk diffusion, diffusion permeability, and osmotic permeability are computed and compared among all models. The results show that there are significant differences between TIP3P (a particularly widespread model for simulations of biological systems) and the more recently developed TIP4P/2005 and OPC models. We demonstrate that OPC and TIP4P/2005 reproduce protein-water interactions and dynamics in very good agreement with experimental data. From this study, we find that the choice of the water model has a significant effect on the computed water dynamics as well as its molecular behavior within a biological nanopore.
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Affiliation(s)
| | - Alberto Zaragoza
- Department of Chemistry, The University of Utah, Salt Lake City, Utah 84112-0850, USA
| | - Charlotte I Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, OX1 3QU Oxford, United Kingdom
| | - Chantal Valeriani
- Universidad Complutense de Madrid, Facultad de Ciencias Fícias, Departamento de Estructura de la Materia, Física Térmica y Electrónica, 28040 Madrid, Spain
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18
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Response of avian communities to edges of tropical montane forests: Implications for the future of endemic habitat specialists. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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19
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Richards JH. Assessing the strength of climate and land-use influences on montane epiphyte communities. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:1496-1506. [PMID: 33294988 DOI: 10.1111/cobi.13679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 11/13/2020] [Accepted: 12/01/2020] [Indexed: 06/12/2023]
Abstract
Epiphytes, air plants that are structurally dependent on trees, are a keystone group in tropical forests; they support the food and habitat needs of animals and influence water and nutrient cycles. They reach peak diversity in humid montane forests. Climate predictions for Central American mountains include increased temperatures, altered precipitation seasonality, and increased cloud base heights, all of which may challenge epiphytes. Although remaining montane forests are highly fragmented, many tropical agricultural systems include trees that host epiphytes, allowing epiphyte communities to persist even in landscapes with lower forest connectivity. I used structural equations models to test the relative effects of climate, land use, tree characteristics, and biotic interactions on vascular epiphyte diversity with data from 31 shade coffee farms and 2 protected forests in northern Nicaragua. I also tested substrate preferences of common species with randomization tests. Tree size, tree diversity, and climate all affected epiphyte richness, but the effect of climate was almost entirely mediated by bryophyte cover. Bryophytes showed strong sensitivity to mean annual temperature and insolation. Many ferns and some orchids were positively associated with bryophyte mats, whereas bromeliads tended to establish among lichen or on bare bark. The tight relationships between bryophytes and climate and between bryophytes and vascular epiphytes indicated that relatively small climate changes could result in rapid, cascading losses of montane epiphyte communities. Currently, shade coffee farms can support high bryophyte cover and diverse vascular epiphyte assemblages when larger, older trees are present. Agroforests serve as valuable reservoirs for epiphyte biodiversity and may be important early-warning systems as the climate changes.
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Affiliation(s)
- Jeannine H Richards
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, Madison, WI, 53706, U.S.A
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20
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Schultze S, Grubmüller H. Time-Lagged Independent Component Analysis of Random Walks and Protein Dynamics. J Chem Theory Comput 2021; 17:5766-5776. [PMID: 34449229 PMCID: PMC8444338 DOI: 10.1021/acs.jctc.1c00273] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
![]()
Time-lagged independent
component analysis (tICA) is a widely used
dimension reduction method for the analysis of molecular dynamics
(MD) trajectories and has proven particularly useful for the construction
of protein dynamics Markov models. It identifies those “slow”
collective degrees of freedom onto which the projections of a given
trajectory show maximal autocorrelation for a given lag time. Here
we ask how much information on the actual protein dynamics and, in
particular, the free energy landscape that governs these dynamics
the tICA-projections of MD-trajectories contain, as opposed to noise
due to the inherently stochastic nature of each trajectory. To answer
this question, we have analyzed the tICA-projections of high dimensional
random walks using a combination of analytical and numerical methods.
We find that the projections resemble cosine functions and strongly
depend on the lag time, exhibiting strikingly complex behavior. In
particular, and contrary to previous studies of principal component
projections, the projections change noncontinuously with increasing
lag time. The tICA-projections of selected 1 μs protein trajectories
and those of random walks are strikingly similar, particularly for
larger proteins, suggesting that these trajectories contain only little
information on the energy landscape that governs the actual protein
dynamics. Further the tICA-projections of random walks show clusters
very similar to those observed for the protein trajectories, suggesting
that clusters in the tICA-projections of protein trajectories do not
necessarily reflect local minima in the free energy landscape. We
also conclude that, in addition to the previous finding that certain
ensemble properties of nonconverged protein trajectories resemble
those of random walks; this is also true for their time correlations.
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Affiliation(s)
- Steffen Schultze
- Max Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany
| | - Helmut Grubmüller
- Max Planck Institute for Biophysical Chemistry, Göttingen, 37077, Germany
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21
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Quintana JF, Field MC. Evolution, function and roles in drug sensitivity of trypanosome aquaglyceroporins. Parasitology 2021; 148:1137-1142. [PMID: 33602349 PMCID: PMC8311954 DOI: 10.1017/s0031182021000354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 12/13/2022]
Abstract
Aquaglyceroporins (AQPs) are membrane proteins that function in osmoregulation and the uptake of low molecular weight solutes, in particular glycerol and urea. The AQP family is highly conserved, with two major subfamilies having arisen very early in prokaryote evolution and retained by eukaryotes. A complex evolutionary history indicates multiple lineage-specific expansions, losses and not uncommonly a complete loss. Consequently, the AQP family is highly evolvable and has been associated with significant events in life on Earth. In the African trypanosomes, a role for the AQP2 paralogue, in sensitivity to two chemotherapeutic agents, pentamidine and melarsoprol, is well established, albeit with the mechanisms for cell entry and resistance unclear until very recently. Here, we discuss AQP evolution, structure and mechanisms by which AQPs impact drug sensitivity, suggesting that AQP2 stability is highly sensitive to mutation while serving as the major uptake pathway for pentamidine.
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Affiliation(s)
- Juan F. Quintana
- Wellcome Centre for Integrative Parasitology (WCIP), Institute of Biodiversity, Animal Health and Comparative Medicine (IBAHCM), University of Glasgow, GlasgowG61 1QH, UK
| | - Mark C. Field
- School of Life Sciences, University of Dundee, DundeeDD1 5EH, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005Ceske Budejovice, Czech Republic
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22
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Wu HC, Yoshioka T, Nakagawa K, Shintani T, Matsuyama H. Water Transport and Ion Diffusion Investigation of an Amphotericin B-Based Channel Applied to Forward Osmosis: A Simulation Study. MEMBRANES 2021; 11:membranes11090646. [PMID: 34564464 PMCID: PMC8467697 DOI: 10.3390/membranes11090646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 08/13/2021] [Accepted: 08/18/2021] [Indexed: 11/17/2022]
Abstract
The use of an Amphotericin B_Ergosterol (AmBEr) channel as an artificial water channel in forward osmosis filtration (FO) was studied via molecular dynamics (MD) simulation. Three channel models were constructed: a common AmBEr channel and two modified C3deOAmB_Ergosterol (C3deOAmBEr) channels with different diameters (12 Å and 18 Å). During FO filtration simulation, the osmotic pressure of salt-water was a driving force for water permeation. We examined the effect of the modified C3deOAmBEr channel on the water transport performance. By tracing the change of the number of water molecules along with simulation time in the saltwater region, the water permeability of the channel models could be calculated. A higher water permeability was observed for a modified C3deOAmBEr channel, and there was no ion permeation during the entire simulation period. The hydrated ions and water molecules were placed into the channel to explore the ion leakage behavior of the channels. The mean squared displacement (MSD) of ions and water molecules was obtained to study the ion leakage performance. The Amphotericin B-based channels showed excellent selectivity of water molecules against ions. The results obtained on an atomistic scale could assist in determining the properties and the optimal filtration applications for Amphotericin B-based channels.
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Affiliation(s)
- Hao-Chen Wu
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Yoshioka
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Correspondence: ; Tel.: +81-78-803-6299
| | - Keizo Nakagawa
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Takuji Shintani
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Graduate School of Science, Technology, and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Hideto Matsuyama
- Research Center for Membrane and Film Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; (H.-C.W.); (K.N.); (T.S.); (H.M.)
- Department of Chemical Science and Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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23
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Nicholls IA, Golker K, Olsson GD, Suriyanarayanan S, Wiklander JG. The Use of Computational Methods for the Development of Molecularly Imprinted Polymers. Polymers (Basel) 2021; 13:2841. [PMID: 34502881 PMCID: PMC8434026 DOI: 10.3390/polym13172841] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/16/2021] [Accepted: 08/19/2021] [Indexed: 12/29/2022] Open
Abstract
Recent years have witnessed a dramatic increase in the use of theoretical and computational approaches in the study and development of molecular imprinting systems. These tools are being used to either improve understanding of the mechanisms underlying the function of molecular imprinting systems or for the design of new systems. Here, we present an overview of the literature describing the application of theoretical and computational techniques to the different stages of the molecular imprinting process (pre-polymerization mixture, polymerization process and ligand-molecularly imprinted polymer rebinding), along with an analysis of trends within and the current status of this aspect of the molecular imprinting field.
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Affiliation(s)
- Ian A. Nicholls
- Bioorganic & Biophysical Chemistry Laboratory, Linnaeus University Centre for Biomaterials Chemistry, Department of Chemistry & Biomedical Sciences, Linnaeus University, SE-391 82 Kalmar, Sweden; (K.G.); (G.D.O.); (S.S.); (J.G.W.)
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24
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Lin R, Zheng J, Pu L, Wang Z, Mei Q, Zhang M, Jian S. Genome-wide identification and expression analysis of aquaporin family in Canavalia rosea and their roles in the adaptation to saline-alkaline soils and drought stress. BMC PLANT BIOLOGY 2021; 21:333. [PMID: 34256694 PMCID: PMC8278772 DOI: 10.1186/s12870-021-03034-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/03/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Canavalia rosea (Sw.) DC. (bay bean) is an extremophile halophyte that is widely distributed in coastal areas of the tropics and subtropics. Seawater and drought tolerance in this species may be facilitated by aquaporins (AQPs), channel proteins that transport water and small molecules across cell membranes and thereby maintain cellular water homeostasis in the face of abiotic stress. In C. rosea, AQP diversity, protein features, and their biological functions are still largely unknown. RESULTS We describe the action of AQPs in C. rosea using evolutionary analyses coupled with promoter and expression analyses. A total of 37 AQPs were identified in the C. rosea genome and classified into five subgroups: 11 plasma membrane intrinsic proteins, 10 tonoplast intrinsic proteins, 11 Nod26-like intrinsic proteins, 4 small and basic intrinsic proteins, and 1 X-intrinsic protein. Analysis of RNA-Seq data and targeted qPCR revealed organ-specific expression of aquaporin genes and the involvement of some AQP members in adaptation of C. rosea to extreme coral reef environments. We also analyzed C. rosea sequences for phylogeny reconstruction, protein modeling, cellular localizations, and promoter analysis. Furthermore, one of PIP1 gene, CrPIP1;5, was identified as functional using a yeast expression system and transgenic overexpression in Arabidopsis. CONCLUSIONS Our results indicate that AQPs play an important role in C. rosea responses to saline-alkaline soils and drought stress. These findings not only increase our understanding of the role AQPs play in mediating C. rosea adaptation to extreme environments, but also improve our knowledge of plant aquaporin evolution more generally.
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Affiliation(s)
- Ruoyi Lin
- Guangdong, Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Jiexuan Zheng
- Guangdong, Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Lin Pu
- Guangdong, Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhengfeng Wang
- Guangdong, Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qiming Mei
- Guangdong, Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Mei Zhang
- Guangdong, Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
| | - Shuguang Jian
- Guangdong, Provincial Key Laboratory of Applied Botany & Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Center for Plant Ecology, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou, 510650, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- CAS Engineering Laboratory for Vegetation Ecosystem Restoration On Islands and Coastal Zones, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
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Venisse JS, Õunapuu-Pikas E, Dupont M, Gousset-Dupont A, Saadaoui M, Faize M, Chen S, Chen S, Petel G, Fumanal B, Roeckel-Drevet P, Sellin A, Label P. Genome-Wide Identification, Structure Characterization, and Expression Pattern Profiling of the Aquaporin Gene Family in Betula pendula. Int J Mol Sci 2021; 22:7269. [PMID: 34298887 PMCID: PMC8304918 DOI: 10.3390/ijms22147269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/29/2021] [Accepted: 06/30/2021] [Indexed: 01/12/2023] Open
Abstract
Aquaporin water channels (AQPs) constitute a large family of transmembrane proteins present throughout all kingdoms of life. They play key roles in the flux of water and many solutes across the membranes. The AQP diversity, protein features, and biological functions of silver birch are still unknown. A genome analysis of Betula pendula identified 33 putative genes encoding full-length AQP sequences (BpeAQPs). They are grouped into five subfamilies, representing ten plasma membrane intrinsic proteins (PIPs), eight tonoplast intrinsic proteins (TIPs), eight NOD26-like intrinsic proteins (NIPs), four X intrinsic proteins (XIPs), and three small basic intrinsic proteins (SIPs). The BpeAQP gene structure is conserved within each subfamily, with exon numbers ranging from one to five. The predictions of the aromatic/arginine selectivity filter (ar/R), Froger's positions, specificity-determining positions, and 2D and 3D biochemical properties indicate noticeable transport specificities to various non-aqueous substrates between members and/or subfamilies. Nevertheless, overall, the BpePIPs display mostly hydrophilic ar/R selective filter and lining-pore residues, whereas the BpeTIP, BpeNIP, BpeSIP, and BpeXIP subfamilies mostly contain hydrophobic permeation signatures. Transcriptional expression analyses indicate that 23 BpeAQP genes are transcribed, including five organ-related expressions. Surprisingly, no significant transcriptional expression is monitored in leaves in response to cold stress (6 °C), although interesting trends can be distinguished and will be discussed, notably in relation to the plasticity of this pioneer species, B. pendula. The current study presents the first detailed genome-wide analysis of the AQP gene family in a Betulaceae species, and our results lay a foundation for a better understanding of the specific functions of the BpeAQP genes in the responses of the silver birch trees to cold stress.
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Affiliation(s)
- Jean-Stéphane Venisse
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Eele Õunapuu-Pikas
- Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia; (E.Õ.-P.); (A.S.)
| | - Maxime Dupont
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Aurélie Gousset-Dupont
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Mouadh Saadaoui
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
- National Institute of Agronomy of Tunisia (INAT), Crop Improvement Laboratory, INRAT, Tunis CP 1004, Tunisia
| | - Mohamed Faize
- Laboratory of Plant Biotechnology, Ecology and Ecosystem Valorization, Faculty of Sciences, University Chouaib Doukkali, El Jadida 24000, Morocco;
| | - Song Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China; (S.C.); (S.C.)
| | - Su Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China; (S.C.); (S.C.)
| | - Gilles Petel
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Boris Fumanal
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Patricia Roeckel-Drevet
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
| | - Arne Sellin
- Institute of Ecology and Earth Sciences, University of Tartu, 51005 Tartu, Estonia; (E.Õ.-P.); (A.S.)
| | - Philippe Label
- Université Clermont Auvergne, INRAE, PIAF, 63000 Clermont-Ferrand, France; (M.D.); (A.G.-D.); (M.S.); (G.P.); (B.F.); (P.R.-D.)
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Limited protection and ongoing loss of tropical cloud forest biodiversity and ecosystems worldwide. Nat Ecol Evol 2021; 5:854-862. [PMID: 33927369 DOI: 10.1038/s41559-021-01450-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 03/22/2021] [Indexed: 02/02/2023]
Abstract
Tropical cloud forests (TCFs) are one of the world's most species- and endemism-rich terrestrial ecosystems. TCFs are threatened by direct human pressures and climate change, yet the fate of these extraordinary ecosystems remains insufficiently quantified. With discussions of the post-2020 biodiversity framework underway, TCFs are a defining test case of the success and promise of recent policy targets and their associated mechanisms to avert the global biodiversity crisis. Here we present a global assessment of the recent status and trends of TCFs and their biodiversity and evaluate the efficacy of current protection measures. We find that cloud forests occupied 0.4% of the global land surface in 2001 and harboured ~3,700 species of birds, mammal, amphibians and tree ferns (~15% of the global diversity of those groups), with half of those species entirely restricted to cloud forests. Worldwide, ~2.4% of cloud forests (in some regions, more than 8%) were lost between 2001 and 2018, especially in readily accessible places. While protected areas have slowed this decline, a large proportion of loss in TCF cover is still occurring despite formal protection. Increased conservation efforts are needed to avert the impending regional or global demise of TCFs and their unique biodiversity.
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27
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Ghorbani M, Wang E, Krämer A, Klauda JB. Molecular dynamics simulations of ethanol permeation through single and double-lipid bilayers. J Chem Phys 2021; 153:125101. [PMID: 33003717 DOI: 10.1063/5.0013430] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Permeation of small molecules through membranes is a fundamental biological process, and molecular dynamics simulations have proven to be a promising tool for studying the permeability of membranes by providing a precise characterization of the free energy and diffusivity. In this study, permeation of ethanol through three different membranes of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylserine (POPS), PO-phosphatidylethanolamine (POPE), and PO-phosphatidylcholine (POPC) is studied. Permeabilities are calculated and compared with two different approaches based on Fick's first law and the inhomogeneous solubility-diffusion model. Microsecond simulation of double bilayers of these membranes provided a direct measurement of permeability by a flux-based counting method. These simulations show that a membrane of POPC has the highest permeability, followed by POPE and POPS. Due to the membrane-modulating properties of ethanol, the permeability increases as functions of concentration and saturation of the inner leaflet in a double bilayer setting, as opposed to the customary definition as a proportionality constant. This concentration dependence is confirmed by single bilayer simulations at different ethanol concentrations ranging from 1% to 18%, where permeability estimates are available from transition-based counting and the inhomogeneous solubility-diffusion model. We show that the free energy and diffusion profiles for ethanol lack accuracy at higher permeant concentrations due to non-Markovian kinetics caused by collective behavior. In contrast, the counting method provides unbiased estimates. Finally, the permeabilities obtained from single bilayer simulations are combined to represent natural gradients felt by a cellular membrane, which accurately models the non-equilibrium effects on ethanol permeability from single bilayer simulations in equilibrium.
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Affiliation(s)
- Mahdi Ghorbani
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Eric Wang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - Andreas Krämer
- Laboratory of Computational Biology, National, Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20824, USA
| | - Jeffery B Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
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Fungal X-Intrinsic Protein Aquaporin from Trichoderma atroviride: Structural and Functional Considerations. Biomolecules 2021; 11:biom11020338. [PMID: 33672420 PMCID: PMC7927018 DOI: 10.3390/biom11020338] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 11/24/2022] Open
Abstract
The major intrinsic protein (MIP) superfamily is a key part of the fungal transmembrane transport network. It facilitates the transport of water and low molecular weight solutes across biomembranes. The fungal uncharacterized X-Intrinsic Protein (XIP) subfamily includes the full protein diversity of MIP. Their biological functions still remain fully hypothetical. The aim of this study is still to deepen the diversity and the structure of the XIP subfamily in light of the MIP counterparts—the aquaporins (AQPs) and aquaglyceroporins (AQGPs)—and to describe for the first time their function in the development, biomass accumulation, and mycoparasitic aptitudes of the fungal bioagent Trichoderma atroviride. The fungus-XIP clade, with one member (TriatXIP), is one of the three clades of MIPs that make up the diversity of T. atroviride MIPs, along with the AQPs (three members) and the AQGPs (three members). TriatXIP resembles those of strict aquaporins, predicting water diffusion and possibly other small polar solutes due to particularly wider ar/R constriction with a Lysine substitution at the LE2 position. The XIP loss of function in ∆TriatXIP mutants slightly delays biomass accumulation but does not impact mycoparasitic activities. ∆TriatMIP forms colonies similar to wild type; however, the hyphae are slightly thinner and colonies produce rare chlamydospores in PDA and specific media, most of which are relatively small and exhibit abnormal morphologies. To better understand the molecular causes of these deviant phenotypes, a wide-metabolic survey of the ∆TriatXIPs demonstrates that the delayed growth kinetic, correlated to a decrease in respiration rate, is caused by perturbations in the pentose phosphate pathway. Furthermore, the null expression of the XIP gene strongly impacts the expression of four expressed MIP-encoding genes of T. atroviride, a plausible compensating effect which safeguards the physiological integrity and life cycle of the fungus. This paper offers an overview of the fungal XIP family in the biocontrol agent T. atroviride which will be useful for further functional analysis of this particular MIP subfamily in vegetative growth and the environmental stress response in fungi. Ultimately, these findings have implications for the ecophysiology of Trichoderma spp. in natural, agronomic, and industrial systems.
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29
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Scholl MA, Bassiouni M, Torres-Sánchez AJ. Drought stress and hurricane defoliation influence mountain clouds and moisture recycling in a tropical forest. Proc Natl Acad Sci U S A 2021; 118:e2021646118. [PMID: 33563756 PMCID: PMC7896295 DOI: 10.1073/pnas.2021646118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Mountain ranges generate clouds, precipitation, and perennial streamflow for water supplies, but the role of forest cover in mountain hydrometeorology and cloud formation is not well understood. In the Luquillo Experimental Forest of Puerto Rico, mountains are immersed in clouds nightly, providing a steady precipitation source to support the tropical forest ecosystems and human uses. A severe drought in 2015 and the removal of forest canopy (defoliation) by Hurricane Maria in 2017 created natural experiments to examine interactions between the living forest and hydroclimatic processes. These unprecedented land-based observations over 4.5 y revealed that the orographic cloud system was highly responsive to local land-surface moisture and energy balances moderated by the forest. Cloud layer thickness and immersion frequency on the mountain slope correlated with antecedent rainfall, linking recycled terrestrial moisture to the formation of mountain clouds; and cloud-base altitude rose during drought stress and posthurricane defoliation. Changes in diurnal cycles of temperature and vapor-pressure deficit and an increase in sensible versus latent heat flux quantified local meteorological response to forest disturbances. Temperature and water vapor anomalies along the mountain slope persisted for at least 12 mo posthurricane, showing that understory recovery did not replace intact forest canopy function. In many similar settings around the world, prolonged drought, increasing temperatures, and deforestation could affect orographic cloud precipitation and the humans and ecosystems that depend on it.
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Affiliation(s)
| | - Maoya Bassiouni
- Department of Crop Production Ecology, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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30
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Daly S, Casey E, Semião AJ. Osmotic backwashing of forward osmosis membranes to detach adhered bacteria and mitigate biofouling. J Memb Sci 2021. [DOI: 10.1016/j.memsci.2020.118838] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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31
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Zangerl-Plessl EM, Lee SJ, Maksaev G, Bernsteiner H, Ren F, Yuan P, Stary-Weinzinger A, Nichols CG. Atomistic basis of opening and conduction in mammalian inward rectifier potassium (Kir2.2) channels. J Gen Physiol 2021; 152:jgp.201912422. [PMID: 31744859 PMCID: PMC7034095 DOI: 10.1085/jgp.201912422] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/30/2019] [Indexed: 12/15/2022] Open
Abstract
This paper presents the crystal structure of a forced open inward rectifier Kir2.2 channel. Molecular dynamics reveals the details of ion permeation through the open channel. Potassium ion conduction through open potassium channels is essential to control of membrane potentials in all cells. To elucidate the open conformation and hence the mechanism of K+ ion conduction in the classic inward rectifier Kir2.2, we introduced a negative charge (G178D) at the crossing point of the inner helix bundle, the location of ligand-dependent gating. This “forced open” mutation generated channels that were active even in the complete absence of phosphatidylinositol-4,5-bisphosphate (PIP2), an otherwise essential ligand for Kir channel opening. Crystal structures were obtained at a resolution of 3.6 Å without PIP2 bound, or 2.8 Å in complex with PIP2. The latter revealed a slight widening at the helix bundle crossing (HBC) through backbone movement. MD simulations showed that subsequent spontaneous wetting of the pore through the HBC gate region allowed K+ ion movement across the HBC and conduction through the channel. Further simulations reveal atomistic details of the opening process and highlight the role of pore-lining acidic residues in K+ conduction through Kir2 channels.
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Affiliation(s)
| | - Sun-Joo Lee
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
| | - Grigory Maksaev
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
| | - Harald Bernsteiner
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Feifei Ren
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
| | - Peng Yuan
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
| | | | - Colin G Nichols
- Department of Cell Biology and Physiology and the Center for Investigation of Membrane Excitability Diseases, Washington University School of Medicine, St. Louis, MO
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32
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Pluhackova K, Horner A. Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity. BMC Biol 2021; 19:4. [PMID: 33441107 PMCID: PMC7807449 DOI: 10.1186/s12915-020-00936-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 11/27/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Lipid-protein interactions stabilize protein oligomers, shape their structure, and modulate their function. Whereas in vitro experiments already account for the functional importance of lipids by using natural lipid extracts, in silico methods lack behind by embedding proteins in single component lipid bilayers. However, to accurately complement in vitro experiments with molecular details at very high spatio-temporal resolution, molecular dynamics simulations have to be performed in natural(-like) lipid environments. RESULTS To enable more accurate MD simulations, we have prepared four membrane models of E. coli polar lipid extract, a typical model organism, each at all-atom (CHARMM36) and coarse-grained (Martini3) representations. These models contain all main lipid headgroup types of the E. coli inner membrane, i.e., phosphatidylethanolamines, phosphatidylglycerols, and cardiolipins, symmetrically distributed between the membrane leaflets. The lipid tail (un)saturation and propanylation stereochemistry represent the bacterial lipid tail composition of E. coli grown at 37∘C until 3/4 of the log growth phase. The comparison of the Simple three lipid component models to the complex 14-lipid component model Avanti over a broad range of physiologically relevant temperatures revealed that the balance of lipid tail unsaturation and propanylation in different positions and inclusion of lipid tails of various length maintain realistic values for lipid mobility, membrane area compressibility, lipid ordering, lipid volume and area, and the bilayer thickness. The only Simple model that was able to satisfactory reproduce most of the structural properties of the complex Avanti model showed worse agreement of the activation energy of basal water permeation with the here performed measurements. The Martini3 models reflect extremely well both experimental and atomistic behavior of the E. coli polar lipid extract membranes. Aquaporin-1 embedded in our native(-like) membranes causes partial lipid ordering and membrane thinning in its vicinity. Moreover, aquaporin-1 attracts and temporarily binds negatively charged lipids, mainly cardiolipins, with a distinct cardiolipin binding site in the crevice at the contact site between two monomers, most probably stabilizing the tetrameric protein assembly. CONCLUSIONS The here prepared and validated membrane models of E. coli polar lipids extract revealed that lipid tail complexity, in terms of double bond and cyclopropane location and varying lipid tail length, is key to stabilize membrane properties over a broad temperature range. In addition, they build a solid basis for manifold future simulation studies on more realistic lipid membranes bridging the gap between simulations and experiments.
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Affiliation(s)
- Kristyna Pluhackova
- Department of Biosystems Science and Engineering, Eidgenössiche Technische Hochschule (ETH) Zürich, Mattenstr. 26, Basel, 4058, Switzerland.
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
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Li F, Egea PF, Vecchio AJ, Asial I, Gupta M, Paulino J, Bajaj R, Dickinson MS, Ferguson-Miller S, Monk BC, Stroud RM. Highlighting membrane protein structure and function: A celebration of the Protein Data Bank. J Biol Chem 2021; 296:100557. [PMID: 33744283 PMCID: PMC8102919 DOI: 10.1016/j.jbc.2021.100557] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/10/2021] [Accepted: 03/16/2021] [Indexed: 12/13/2022] Open
Abstract
Biological membranes define the boundaries of cells and compartmentalize the chemical and physical processes required for life. Many biological processes are carried out by proteins embedded in or associated with such membranes. Determination of membrane protein (MP) structures at atomic or near-atomic resolution plays a vital role in elucidating their structural and functional impact in biology. This endeavor has determined 1198 unique MP structures as of early 2021. The value of these structures is expanded greatly by deposition of their three-dimensional (3D) coordinates into the Protein Data Bank (PDB) after the first atomic MP structure was elucidated in 1985. Since then, free access to MP structures facilitates broader and deeper understanding of MPs, which provides crucial new insights into their biological functions. Here we highlight the structural and functional biology of representative MPs and landmarks in the evolution of new technologies, with insights into key developments influenced by the PDB in magnifying their impact.
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Affiliation(s)
- Fei Li
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA; Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Pascal F Egea
- Department of Biological Chemistry, School of Medicine, University of California Los Angeles, Los Angeles, California, USA
| | - Alex J Vecchio
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | | | - Meghna Gupta
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Joana Paulino
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Ruchika Bajaj
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Miles Sasha Dickinson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, USA
| | - Brian C Monk
- Sir John Walsh Research Institute and Department of Oral Sciences, University of Otago, North Dunedin, Dunedin, New Zealand
| | - Robert M Stroud
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, USA.
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34
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Zhang QL, Wu YX, Yang RY, Zhang JL, Wang RF. Effect of the direction of static electric fields on water transport through nanochannels. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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35
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Sakashita N, Ishikita H, Saito K. Rigidly hydrogen-bonded water molecules facilitate proton transfer in photosystem II. Phys Chem Chem Phys 2020; 22:15831-15841. [PMID: 32613215 DOI: 10.1039/d0cp00295j] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In the water-splitting enzyme photosystem II (PSII), the proton is released from the catalytic site and transferred to the protein bulk surface via the proton-relay mechanism. Proton transfer occurs in a proton-conducting channel consisting of a series of water molecules connected by hydrogen-bonded (H-bonded) chains. The water-transport protein aquaporin (AQP) also contains a water chain with structure similar to that of the PSII proton channel, although the water chain does not transport protons. We compared the PSII proton channel with the AQP water channel from the following standpoints: (1) the energetics of proton transfer based on crystal structures obtained from quantum mechanical/molecular mechanical calculations, and (2) fluctuations in water molecules obtained from molecular dynamics simulations. The results showed that residues facing the channel and acting as H-bonded partners of water molecules predominantly determined the proton-transfer ability. In PSII, the water chain is surrounded by H-bond acceptors (e.g., carbonyl groups), and the water chain transports protons where the water molecules are rigidly fixed. In AQP, the water chain is surrounded by hydrophobic sidechains or H-bond donors (e.g., NH2 groups), and it does not transport protons where the water molecules are flexible and fluctuating.
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Affiliation(s)
- Naoki Sakashita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan
| | - Hiroshi Ishikita
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan and Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
| | - Keisuke Saito
- Department of Applied Chemistry, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8654, Japan and Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
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Rahimi Z, Lohrasebi A. Influences of electric fields on the operation of Aqy1 aquaporin channels: a molecular dynamics study. Phys Chem Chem Phys 2020; 22:25859-25868. [PMID: 33155592 DOI: 10.1039/d0cp04763e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The dynamics of water molecules inside an Aquaporin channel, embedded within a stochastically fluctuating membrane, was modeled by means of the application of the molecular dynamics (MD) simulation method. We considered the effect of the existence and nonexistence of an external electric field, either constant or oscillating, on the stability of the channel. It was observed that the permeation of water molecules through the channel was increased when the channel was exposed to a constant electric field of strength -0.2 mV nm-1. Moreover, oscillating electric fields of 5 and 10 GHz frequencies, which is the range of field frequency generally present in our daily life, were applied to the channel, showing not significant effects on the stability of the channel and its important parts. In addition, we investigated the influence of the application of electric fields on the water molecule ordinations in the channels, and the results showed that the water molecule orientations were changed in response to the applied field.
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Affiliation(s)
- Z Rahimi
- Department of Physics, University of Isfahan, P.O. Box 81746-73441, Isfahan, Iran.
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37
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Jia Y, Lu X, Cao Z, Yan T. From a bulk to nanoconfined water chain: bridge water at the pore of the (6,6) carbon nanotube. Phys Chem Chem Phys 2020; 22:25747-25759. [PMID: 33146653 DOI: 10.1039/d0cp02531c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrophobic porous materials with nano-pores are critical in many processes such as water desalination and biological membrane transportation. Herein, we performed molecular dynamics (MD) simulations on a prototypical hydrophobic nanochannel consisting of a (6,6) carbon nanotube (CNT) of 4.12 Å in radius and 13.72 Å in length immersed in water. The simulation shows that there are two major filling numbers of water N = 5 and N = 6, with the former being the most stable one. The confined waters form a single-file water chain with two hydrogen bonds per water. An extending water chain is formed for N = 5, with a bridge water near the pore of the CNT linking the water confined inside the CNT and hydration layer around the pore of the CNT. The bridge water can be considered as intermediate water characterized by three hydrogen bonds that distinguish from the confined water and bulk water. On the other hand, the hydration layer is depleted from the pore when N = 6. The analyses of the correlation of the bond order for the adjacent hydrogen bond pair of the hydration layer around the pore of the CNT does not show apparent difference from that of bulk water, though the former is slightly ordered. van Hove analysis of the bridge water shows that it tends to move inside the CNT when N < 5, in order to maintain the chemical equilibrium between the confined water and bulk water. This study highlights the unique structure of water around the hydrophobic pore of a sub-nanometer nanochannel.
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Affiliation(s)
- Yunzhe Jia
- Institute of New Energy Material Chemistry, School of Materials Science and Engineering, Nankai University, Tianjin 300350, China.
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38
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Liu P, Lai H, Luo X, Xia Q, Zhang D, Cheng Z, Liu Y, Jiang L. Superlyophilic Shape Memory Porous Sponge for Smart Liquid Permeation. ACS NANO 2020; 14:14047-14056. [PMID: 32970408 DOI: 10.1021/acsnano.0c06673] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Recently, smart liquid permeation has aroused much attention. However, existing strategies to achieve such a goal are often based on reversibly controlling hydrophobicity/hydrophilicity on static porous structures, which are unsuitable for oils with low surface tension, and meanwhile they cannot realize tunable permeation flux since the pore sizes are constant. Herein, we report a superlyophilic shape memory porous sponge (SSMS) that can demonstrate tunable pore size from about 28 nm to 900 μm as the material's shape is changed. Based on the controllability in pore size, not only ON/OFF penetration but also precisely tunable permeation flux can be obtained for both water and oil. Furthermore, by using the SSMS, an application in accurate release of small-molecule rhodamine B was also demonstrated. This work reports a material with tunable pore size for controllable liquid permeation, which provides some ideas for designing smart superwetting permeation materials.
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Affiliation(s)
- Pengchang Liu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Hua Lai
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Xin Luo
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Qixing Xia
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Dongjie Zhang
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Zhongjun Cheng
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Yuyan Liu
- MIIT Key Laboratory of Critical Materials Technology for New Energy Conversion and Storage, School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin 150001, People's Republic of China
| | - Lei Jiang
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China
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The Ionophores CCCP and Gramicidin but Not Nigericin Inhibit Trypanosoma brucei Aquaglyceroporins at Neutral pH. Cells 2020; 9:cells9102335. [PMID: 33096791 PMCID: PMC7589649 DOI: 10.3390/cells9102335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 10/16/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022] Open
Abstract
Human African trypanosomiasis (HAT) is caused by Trypanosoma brucei parasites. The T. brucei aquaglyceroporin isoform 2, TbAQP2, has been linked to the uptake of pentamidine. Negative membrane potentials and transmembrane pH gradients were suggested to promote transport of the dicationic antitrypanosomal drug. Application of ionophores to trypanosomes further hinted at direct inhibition of TbAQP2 by carbonyl cyanide m-chlorophenyl hydrazone (CCCP). Here, we tested for direct effects of three classical ionophores (CCCP, nigericin, gramicidin) on the functionality of TbAQP2 and the related TbAQP3 at conditions that are independent from the membrane potential or a proton gradient. We expressed TbAQP2 and TbAQP3 in yeast, and determined permeability of uncharged glycerol at neutral pH using stopped-flow light scattering. The mobile proton carrier CCCP directly inhibited TbAQP2 glycerol permeability at an IC50 of 2 µM, and TbAQP3 to a much lesser extent (IC50 around 1 mM) likely due to different selectivity filter layouts. Nigericin, another mobile carrier, left both isoforms unaffected. The membrane-integral pore-forming gramicidin evenly inhibited TbAQP2 and TbAQP2 in the double-digit micromolar range. Our data exemplify the need for suitable controls to detect unwanted ionophore side effects even when used at concentrations that are typically recommended to disturb the transmembrane ion distribution.
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40
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Mom R, Muries B, Benoit P, Robert-Paganin J, Réty S, Venisse JS, Padua A, Label P, Auguin D. Voltage-gating of aquaporins, a putative conserved safety mechanism during ionic stresses. FEBS Lett 2020; 595:41-57. [PMID: 32997337 DOI: 10.1002/1873-3468.13944] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 09/19/2020] [Indexed: 11/10/2022]
Abstract
Aquaporins are transmembrane water channels found in almost every living organism. Numerous studies have brought a good understanding of both water transport through their pores and the regulations taking place at the molecular level, but subtleties remain to be clarified. Recently, a voltage-related gating mechanism involving the conserved arginine of the channel's main constriction was captured for human aquaporins through molecular dynamics studies. With a similar approach, we show that this voltage-gating could be conserved among this family and that the underlying mechanism could explain part of plant AQPs diversity when contextualized to high ionic concentrations provoked by drought. Finally, we identified residues as adaptive traits which constitute good targets for drought resistance plant breeding research.
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Affiliation(s)
- Robin Mom
- UCA, INRAE, UMR PIAF, Clermont-Ferrand, France
| | | | | | - Julien Robert-Paganin
- Structural Motility, Institut Curie, Paris Université Sciences et Lettres, CNRS UMR144, Sorbonne Université, Paris, France
| | - Stéphane Réty
- Laboratoire de Biologie et Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, INSERM U1210, University Claude Bernard, Lyon, France
| | | | - Agilio Padua
- Laboratoire de Chimie, ENS de Lyon, CNRS, Université de Lyon, Lyon, France
| | | | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, UPRES EA 1207, INRAE-USC1328, Université d'Orléans, Orléans, France
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Hadidi H, Kamali R, Binesh A. Dynamics and energetics of water transport through aquaporin mutants causing nephrogenic diabetes insipidus (NDI): A molecular dynamics study. J Biomol Struct Dyn 2020; 40:1273-1284. [PMID: 33030091 DOI: 10.1080/07391102.2020.1824813] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human aquaporin-2 (AQP2) is the principal water channel in the human kidney. Any alteration of its physiological functioning may lead to the water imbalance and consequently diseases in humans, especially nephrogenic diabetes insipidus (NDI). Although many of the mutations associated with NDI are experimentally discovered and examined, a molecular level characterization of the structure and transport mechanism is still missing. In this paper, the gating effects of selectivity filter (SF) as wide/narrow states on the mechanism and dynamics of water permeation within the wild-type AQP2 and two NDI causing mutants as AQP2-V168M and AQP2-G64R are studied for the first time. The analysis of the 200 ns trajectory shows that the SF region in AQP2 is not only a selectivity filter, as previously reported but also it performs as a gating site depending on the side-chain conformation of His172. The assignment of the wide/narrow states of SF is supported by computing the free energy and permeability through the AQP2. Moreover, by exploring the effects of V168M and G64R mutants on the AQP2 structure during 200 ns trajectories, remarkable increases of energy barriers are observed in the middle and cytoplasmic side of the pore, respectively. Interestingly, it is found that due to the variable conformations of the SF region as wide/narrow, the effect of the NDI causing mutants on the average water permeability can be revealed with notably better accuracy by finding the wide states in the wild-type and mutated types of AQP2 and comparing the osmotic permeabilities for this state.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hooman Hadidi
- Department of Mechanical Engineering, Shiraz University, Shiraz, Fars, Iran
| | - Reza Kamali
- Department of Mechanical Engineering, Shiraz University, Shiraz, Fars, Iran
| | - Alireza Binesh
- Department of Hydro-Aerodynamics, Malek-e-Ashtar University of Technology, Shiraz, Iran
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42
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Quantitative Synaptic Biology: A Perspective on Techniques, Numbers and Expectations. Int J Mol Sci 2020; 21:ijms21197298. [PMID: 33023247 PMCID: PMC7582872 DOI: 10.3390/ijms21197298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 12/31/2022] Open
Abstract
Synapses play a central role for the processing of information in the brain and have been analyzed in countless biochemical, electrophysiological, imaging, and computational studies. The functionality and plasticity of synapses are nevertheless still difficult to predict, and conflicting hypotheses have been proposed for many synaptic processes. In this review, we argue that the cause of these problems is a lack of understanding of the spatiotemporal dynamics of key synaptic components. Fortunately, a number of emerging imaging approaches, going beyond super-resolution, should be able to provide required protein positions in space at different points in time. Mathematical models can then integrate the resulting information to allow the prediction of the spatiotemporal dynamics. We argue that these models, to deal with the complexity of synaptic processes, need to be designed in a sufficiently abstract way. Taken together, we suggest that a well-designed combination of imaging and modelling approaches will result in a far more complete understanding of synaptic function than currently possible.
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Krämer A, Ghysels A, Wang E, Venable RM, Klauda JB, Brooks BR, Pastor RW. Membrane permeability of small molecules from unbiased molecular dynamics simulations. J Chem Phys 2020; 153:124107. [PMID: 33003739 PMCID: PMC7519415 DOI: 10.1063/5.0013429] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
Permeation of many small molecules through lipid bilayers can be directly observed in molecular dynamics simulations on the nano- and microsecond timescale. While unbiased simulations provide an unobstructed view of the permeation process, their feasibility for computing permeability coefficients depends on various factors that differ for each permeant. The present work studies three small molecules for which unbiased simulations of permeation are feasible within less than a microsecond, one hydrophobic (oxygen), one hydrophilic (water), and one amphiphilic (ethanol). Permeabilities are computed using two approaches: counting methods and a maximum-likelihood estimation for the inhomogeneous solubility diffusion (ISD) model. Counting methods yield nearly model-free estimates of the permeability for all three permeants. While the ISD-based approach is reasonable for oxygen, it lacks precision for water due to insufficient sampling and results in misleading estimates for ethanol due to invalid model assumptions. It is also demonstrated that simulations using a Langevin thermostat with collision frequencies of 1/ps and 5/ps yield oxygen permeabilities and diffusion constants that are lower than those using Nosé-Hoover by statistically significant margins. In contrast, permeabilities from trajectories generated with Nosé-Hoover and the microcanonical ensemble do not show statistically significant differences. As molecular simulations become more affordable and accurate, calculation of permeability for an expanding range of molecules will be feasible using unbiased simulations. The present work summarizes theoretical underpinnings, identifies pitfalls, and develops best practices for such simulations.
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Affiliation(s)
- Andreas Krämer
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - An Ghysels
- IBiTech - BioMMeda, Ghent University, Corneel Heymanslaan 10, Block B - Entrance 36, 9000 Gent, Belgium
| | - Eric Wang
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, USA
| | - Richard M. Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Jeffery B. Klauda
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20740, USA
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Richard W. Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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Rodriguez RA, Chan R, Liang H, Chen LY. Quantitative study of unsaturated transport of glycerol through aquaglyceroporin that has high affinity for glycerol. RSC Adv 2020; 10:34203-34214. [PMID: 32944226 PMCID: PMC7494219 DOI: 10.1039/d0ra05262k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/08/2020] [Indexed: 11/21/2022] Open
Abstract
The structures of several aquaglyceroporins have been resolved to atomic resolution showing two or more glycerols bound inside a channel and confirming a glycerol-facilitator's affinity for its substrate glycerol. However, the kinetics data of glycerol transport experiments all point to unsaturated transport that is characteristic of low substrate affinity in terms of the Michaelis-Menten kinetics. In this article, we present an in silico-in vitro research focused on AQP3, one of the human aquaglyceroporins that is natively expressed in the abundantly available erythrocytes. We conducted 2.1 μs in silico simulations of AQP3 embedded in a model erythrocyte membrane with intracellular-extracellular asymmetries in leaflet lipid compositions and compartment salt ions. From the equilibrium molecular dynamics (MD) simulations, we elucidated the mechanism of glycerol transport at high substrate concentrations. From the steered MD simulations, we computed the Gibbs free-energy profile throughout the AQP3 channel. From the free-energy profile, we quantified the kinetics of glycerol transport that is unsaturated due to glycerol-glycerol interactions mediated by AQP3 resulting in the concerted movement of two glycerol molecules for the transport of one glycerol molecule across the cell membrane. We conducted in vitro experiments on glycerol uptake into human erythrocytes for a wide range of substrate concentrations and various temperatures. The experimental data quantitatively validated our theoretical-computational conclusions on the unsaturated glycerol transport through AQP3 that has high affinity for glycerol.
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Affiliation(s)
- Roberto A. Rodriguez
- Department of Physics, The University of Texas at San AntonioSan AntonioTexas 78249USA
| | - Ruth Chan
- Department of Physics, The University of Texas at San AntonioSan AntonioTexas 78249USA
| | - Huiyun Liang
- Department of Physics, The University of Texas at San AntonioSan AntonioTexas 78249USA
- Department of Pharmacology, The University of Texas Health Science Center at San AntonioSan AntonioTexas 78229USA
| | - Liao Y. Chen
- Department of Physics, The University of Texas at San AntonioSan AntonioTexas 78249USA
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Insights into the Selectivity Mechanisms of Grapevine NIP Aquaporins. Int J Mol Sci 2020; 21:ijms21186697. [PMID: 32933135 PMCID: PMC7576499 DOI: 10.3390/ijms21186697] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/05/2020] [Accepted: 09/10/2020] [Indexed: 12/11/2022] Open
Abstract
Nodulin 26-like intrinsic proteins (NIPs) of the plant aquaporin family majorly facilitate the transport of physiologically relevant solutes. The present study intended to investigate how substrate selectivity in grapevine NIPs is influenced by the aromatic/arginine (ar/R) selectivity filter within the pore and the possible underlying mechanisms. A mutational approach was used to interchange the ar/R residues between grapevine NIPs (VvTnNIP1;1 with VvTnNIP6;1, and VvTnNIP2;1 with VvTnNIP5;1). Their functional characterization by stopped-flow spectroscopy in Saccharomyces cerevisiae revealed that mutations in residues of H2/H5 helices in VvTnNIP1;1 and VvTnNIP6;1 caused a general decline in membrane glycerol permeability but did not impart the expected substrate conductivity in the mutants. This result suggests that ar/R filter substitution could alter the NIP channel activity, but it was not sufficient to interchange their substrate preferences. Further, homology modeling analyses evidenced that variations in the pore radius combined with the differences in the channel's physicochemical properties (hydrophilicity/hydrophobicity) may drive substrate selectivity. Furthermore, yeast growth assays showed that H5 residue substitution alleviated the sensitivity of VvTnNIP2;1 and VvTnNIP5;1 to As, B, and Se, implying importance of H5 sequence for substrate selection. These results contribute to the knowledge of the overall determinants of substrate selectivity in NIPs.
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47
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Jia Y, Liu X. Polyploidization and pseudogenization in allotetraploid frog Xenopus laevis promote the evolution of aquaporin family in higher vertebrates. BMC Genomics 2020; 21:525. [PMID: 32727380 PMCID: PMC7392679 DOI: 10.1186/s12864-020-06942-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/23/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Aquaporins (AQPs), as members of the major intrinsic protein (MIP) superfamily, facilitated the permeation of water and other solutes and are involved in multiple biological processes. AQP family exists in almost all living organisms and is highly diversified in vertebrates in both classification and function due to genome wide duplication. While some AQP orthologs have been lost in higher vertebrates through evolution. RESULT Genome-wide comparative analyses of the AQP family between allotetraploid frog Xenopus laevis (Xla) and diploid frog Xenopus tropicalis (Xtr), based on the genome assemblies, revealed that the number of AQPs in Xla genome nearly doubled that in Xtr (32 vs. 19). Synteny analysis indicated that the distribution of the retained AQPs in Xla subgenomes (17 in Xla. L, the longer homeolog of Xla genome and 15 in Xla. S, the shorter homeolog of Xla genome) were highly symmetrical when compared with that in Xtr genome. Remarkably, two members in Xla. L and four members in Xla. S were lost through evolution. Blast analysis revealed that the lost AQPs in Xla are pseudogenized via either the deletion of some exons or some single nucleotide insertions or deletions that lead the reading frame shift. Additionally, comparative genomic analyses suggested that the orthologs of AQPs that with one copy absence in Xla are also prone to be lost in higher vertebrates. CONCLUSION This study revealed that polyploidization and subsequent pseudogenization and deletion in Xla genome promote the evolution of AQP family in higher vertebrates. Besides, our results would also contribute to understanding the evolution of AQP family.
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Affiliation(s)
- Yanglei Jia
- Fishery College of Zhejiang Ocean University, Key Laboratory of Marine Fishery Equipment and Technology of Zhejiang, Zhoushan, Zhejiang, China
| | - Xiao Liu
- Fishery College of Zhejiang Ocean University, Key Laboratory of Marine Fishery Equipment and Technology of Zhejiang, Zhoushan, Zhejiang, China.
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Moss FJ, Mahinthichaichan P, Lodowski DT, Kowatz T, Tajkhorshid E, Engel A, Boron WF, Vahedi-Faridi A. Aquaporin-7: A Dynamic Aquaglyceroporin With Greater Water and Glycerol Permeability Than Its Bacterial Homolog GlpF. Front Physiol 2020; 11:728. [PMID: 32695023 PMCID: PMC7339978 DOI: 10.3389/fphys.2020.00728] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 06/04/2020] [Indexed: 12/27/2022] Open
Abstract
Xenopus oocytes expressing human aquaporin-7 (AQP7) exhibit greater osmotic water permeability and 3H-glycerol uptake vs. those expressing the bacterial glycerol facilitator GlpF. AQP7-expressing oocytes exposed to increasing extracellular [glycerol] under isosmolal conditions exhibit increasing swelling rates, whereas GlpF-expressing oocytes do not swell at all. To provide a structural basis for these observed physiological differences, we performed X-ray crystallographic structure determination of AQP7 and molecular-dynamics simulations on AQP7 and GlpF. The structure reveals AQP7 tetramers containing two monomers with 3 glycerols, and two monomers with 2 glycerols in the pore. In contrast to GlpF, no glycerol is bound at the AQP7 selectivity filter (SF), comprising residues F74, G222, Y223, and R229. The AQP7 SF is resolved in its closed state because F74 blocks the passage of small solutes. Molecular dynamics simulations demonstrate that F74 undergoes large and rapid conformational changes, allowing glycerol molecules to permeate without orientational restriction. The more rigid GlpF imposes orientational constraints on glycerol molecules passing through the SF. Moreover, GlpF-W48 (analogous to AQP7-F74) undergoes rare but long-lasting conformational changes that block the pore to H2O and glycerol.
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Affiliation(s)
- Fraser J. Moss
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Paween Mahinthichaichan
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - David T. Lodowski
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Thomas Kowatz
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Quantitative Biology, and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Andreas Engel
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Walter F. Boron
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
| | - Ardeschir Vahedi-Faridi
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
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Ozyigit II, Filiz E, Saracoglu IA, Karadeniz S. Exploration of two major boron transport genes BOR1 and NIP5;1 in the genomes of different plants. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1773311] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Ibrahim Ilker Ozyigit
- Department of Biology, Faculty of Science and Arts, Marmara University, Goztepe, Istanbul, Turkey
- Department of Biology, Faculty of Science, Kyrgyz-Turkish Manas University, Bishkek, Kyrgyzstan
| | - Ertugrul Filiz
- Department of Crop and Animal Production, Cilimli Vocational School, Duzce University, Duzce, Turkey
| | - Ibrahim Adnan Saracoglu
- Department of Chemistry, Faculty of Science and Arts, Marmara University, Goztepe, Istanbul, Turkey
- Presidancy of the Republic of Turkey, Ankara, Turkey
| | - Sedat Karadeniz
- Department of Biology, Faculty of Science and Arts, Marmara University, Goztepe, Istanbul, Turkey
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Chan R, Falato M, Liang H, Chen LY. In silico simulations of erythrocyte aquaporins with quantitative in vitro validation. RSC Adv 2020; 10:21283-21291. [PMID: 32612811 PMCID: PMC7328926 DOI: 10.1039/d0ra03456h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Modelling water and membrane lipids is an essential element in the computational research of biophysical/biochemical processes such as water transport across the cell membrane. In this study, we examined the accuracies of two popular water models, TIP3P and TIP4P, in the molecular dynamics simulations of erythrocyte aquaporins (AQP1 and AQP3). We modelled the erythrocyte membrane as an asymmetric lipid bilayer with appropriate lipid compositions of its inner and outer leaflet, in comparison with a symmetric lipid bilayer of a single lipid type. We computed the AQP1/3 permeabilities with the transition state theory with full correction for recrossing events. We also conducted cell swelling assays for water transport across the erythrocyte membrane. The experimental results agree with the TIP3P water–erythrocyte membrane model, in confirmation of the expected accuracy of the erythrocyte membrane model, the TIP3P water model, and the CHARMM parameters for water–protein interactions. Quantitatively predictive study of aquaporins in model erythrocyte membrane validated with cellular experiments.![]()
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Affiliation(s)
- Ruth Chan
- Department of Physics, The University of Texas at San Antonio, San Antonio, Texas 78249 USA
| | - Michael Falato
- Department of Physics, The University of Texas at San Antonio, San Antonio, Texas 78249 USA
| | - Huiyun Liang
- Department of Physics, The University of Texas at San Antonio, San Antonio, Texas 78249 USA.,Department of Pharmacology, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229 USA
| | - Liao Y Chen
- Department of Physics, The University of Texas at San Antonio, San Antonio, Texas 78249 USA
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